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Subject: Re: [OMPI users] uninstall
From: Gus Correa (gus_at_[hidden])
Date: 2009-06-10 12:45:01

Hi Jacob

Besides Ralph's suggestion,
see these FAQs (# 4 and # 5):

Easy way is to install on an NFS mounted directory on all computers.
This way only one installation is needed (e.g.
/share/apps/openmpi-1.3.2, which
is a typical shared directory name if you use Rocks clusters).

Another way is to install on a directory with the same name on each
computer (e.g. /opt/openmpi-1.3.2, every computer has its own /opt).
This way you have to install on every computer (or copy over the whole
OpenMPI directory tree to all of them, if the computers have the same

Use the configure --prefix=/directory/name to choose the installation
Don't choose the standard locations /usr or /usr/local, as it may
overwrite existing MPIs and mess things up with yum.

I hope this helps.
Gus Correa
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA

Ralph Castain wrote:
> When you built OMPI from hand, you probably configured it with a
> --prefix=foo option. Just "rm -rf foo" to uninstall, and then make sure
> your PATH and LD_LIBRARY_PATH don't include "foo" any more if you
> modified your .login and/or .cshrc files (or whatever you use).
> On Jun 10, 2009, at 1:11 AM, Jacob Balthazor wrote:
>> Hey,
>> I downloaded compiled, and installed open mpi off the web site but
>> was having problems. I then installed open mpi and ins libs via yum.
>> Adter that I was able to compile and run mpi programs locally but ran
>> into problems when I tried to run them across two computers (see
>> output below). I was told that this was probably because I have two
>> different copies of openmpi. I uninstalled openmpi via yum and am now
>> trying to figure out the best way to uninstall the compiled version of
>> openmpi to reinstall with a clean slate. Any suggestions?
>> -Jacob
>> On Jun 2, 2009, at 4:45 AM, Jeff Squyres wrote:
>> This looks like you have two different versions of Open MPI installed
>> on your two machines (it's hard to tell with the name
>> "localhost.localdomain", though -- can you name your two computers
>> differently so that you can tell them apart in the output?).
>> You need to have the same version of Open MPI installed on both machines.
>> On Jun 2, 2009, at 3:52 AM, jacob Balthazor wrote:
>>> Hi,
>>> I am just getting my feet wet with openmpi and can't seem to get
>>> it running. I installed openmpi and all it's components via yum and
>>> am able compile and run programs with mpi locally but not across the
>>> two computers. I set up the keyed ssh on both mechines and am able to
>>> log into another without asking for a password. From reading online
>>> it looks like my problem may stem from an unconfigured .bash_profile
>>> as I don't think yum would have configured it for me. My question is
>>> where does yum stick the bin and lib files that I need to reference
>>> in my profile? What should my bash_profile look like? Thank you for
>>> reading and am eagerly awaiting your reply.
>>> -Jacob
>>> My Profile:
>>> # .bash_profile
>>> # Get the aliases and functions
>>> if [ -f ~/.bashrc ]; then
>>> . ~/.bashrc
>>> fi
>>> # User specific environment and startup programs
>>> PATH=$PATH:$HOME/bin
>>> export PATH
>>> When I try to run it:
>>> [beowulf2_at_localhost Desktop]$ mpirun --hostfile hostfile -np 4 a.out
>>> [localhost.localdomain:08564] Error: unknown option "--bootproxy"
>>> input in flex scanner failed
>>> [localhost.localdomain:06428] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>>> base/pls_base_orted_cmds.c at line 275
>>> [localhost.localdomain:06428] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>>> pls_rsh_module.c at line 1166
>>> [localhost.localdomain:06428] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>>> errmgr_hnp.c at line 90
>>> [localhost.localdomain:06428] ERROR: A daemon on node
>>> failed to start as expected.
>>> [localhost.localdomain:06428] ERROR: There may be more information
>>> available from
>>> [localhost.localdomain:06428] ERROR: the remote shell (see above).
>>> [localhost.localdomain:06428] ERROR: The daemon exited unexpectedly
>>> with status 2.
>>> [localhost.localdomain:06428] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>>> base/pls_base_orted_cmds.c at line 188
>>> [localhost.localdomain:06428] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>>> pls_rsh_module.c at line 1198
>>> ------------------------------
>>> --------------------------------------------
>>> mpirun was unable to cleanly terminate the daemons for this job.
>>> Returned value Timeout instead of ORTE_SUCCESS.
>>> --------------------------------------------------------------------------
>>> [beowulf2_at_localhost Desktop]$
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